General Overview
IMAP stands for Integrated Microbiome
Analysis Pipelines, developed independenly as standalone GitHub
repositories. When used sequentially, all IMAP parts provide a
systematic microbiome data analysis beyond the traditional methods.
Repo-specific RMD Chunks
Chunk 01
Chunk 02
Chunk 03
References
[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C.,
Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated
bioinformatics and visualization pipeline for microbiome data analysis.
BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4
Appendix
Project main tree
.
├── LICENSE
├── README.md
├── config
│  ├── config.yml
│  ├── pbs
│  ├── samples.tsv
│  ├── slurm
│  └── units.tsv
├── dags
├── data
├── images
│  ├── bkgd.png
│  ├── cicd.png
│  ├── imap.png
│  └── smkreport
├── index.Rmd
├── library
│  ├── apa.csl
│  ├── imap.bib
│  └── references.bib
├── report
│  └── report.html
├── report.html
├── requirements.txt
├── resources
├── results
│  └── project_tree.txt
├── styles.css
├── templates
└── workflow
├── Snakefile
├── envs
├── rules
├── schemas
└── scripts
18 directories, 18 files
Screenshot of interactive snakemake report
The interactive snakemake HTML report can be viewed by opening the
report.htmlusing any compatible browser. You will be able to explore the workflow and the associated statistics. You can close the left bar to get a more expansive display view.
Troubleshooting of FAQs
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Answer
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